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https://github.com/stephenturner/qqman
An R package for creating Q-Q and manhattan plots from GWAS results
https://github.com/stephenturner/qqman
cran genomics gwas r
Last synced: 6 days ago
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An R package for creating Q-Q and manhattan plots from GWAS results
- Host: GitHub
- URL: https://github.com/stephenturner/qqman
- Owner: stephenturner
- License: gpl-3.0
- Created: 2013-04-02T10:45:40.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2024-03-18T16:56:08.000Z (8 months ago)
- Last Synced: 2024-10-28T17:24:51.975Z (9 days ago)
- Topics: cran, genomics, gwas, r
- Language: HTML
- Homepage: http://cran.r-project.org/web/packages/qqman/
- Size: 17.5 MB
- Stars: 156
- Watchers: 16
- Forks: 92
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# qqman: An R package for creating Q-Q and manhattan plots from GWAS results.
[](https://cran.r-project.org/package=qqman)
[](https://doi.org/10.21105/joss.00731)
## Citation
If you'd like to cite qqman (appreciated but not required), please cite the publication below:
Turner, (2018). qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. _Journal of Open Source Software_, 3(25), 731, https://doi.org/10.21105/joss.00731
More details are found in the preprint:
Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. [*biorXiv* DOI: 10.1101/005165](https://biorxiv.org/content/early/2014/05/14/005165).
## Installation
Install the stable release from CRAN:
```r
install.packages("qqman")
```
Or install directly from github using devtools
```r
library(devtools)
install_github("stephenturner/qqman")
```
Or install the most recent development release with devtools (note, there be dragons here):
```r
library(devtools)
install_github("stephenturner/qqman", ref="dev")
```
Load the package each time you use it:
```r
library(qqman)
```
## Usage
See the [online package vignette](https://cran.r-project.org/package=qqman/vignettes/qqman.html) for more examples:
```r
browseVignettes("qqman")
```
Take a look at the built-in data:
```r
head(gwasResults)
```
Basic manhattan plot using built-in data:
```r
manhattan(gwasResults)
```
Basic Q-Q plot using built-in data:
```r
qq(gwasResults$P)
```
Get help:
```r
?manhattan
?qq
```
## Notes
* This release is substantially simplified for the sake of maintainability and creating an R package. The old code that allows confidence intervals on the Q-Q plot and allows more flexible annotation and highlighting is still available at the [version 0.0.0 tag](https://github.com/stephenturner/qqman/tree/v0.0.0).
* Special thanks to Dan Capurso and Tim Knutsen for useful contributions and bugfixes.
* Thanks to all the blog commenters for pointing out bugs and other issues.